Camelia, the Perl 6 bug

IRC log for #bioclipse, 2012-06-21

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary

All times shown according to UTC.

Time Nick Message
02:50 ChanServ joined #bioclipse
05:25 sneumann_ joined #bioclipse
05:31 olass joined #bioclipse
06:38 Gpox joined #bioclipse
06:45 egonw_ joined #bioclipse
06:48 olass joined #bioclipse
07:08 olass joined #bioclipse
07:12 olass joined #bioclipse
07:16 sneumann_ moin everyone
07:19 egonw_ hi sneumann_
07:33 CIA-99 bioclipse.cheminformatics: Arvid Berg 2.5.x * re8aecb5 / plugins/net.bioclipse.cdk.ui/src/net/biocli​pse/cdk/ui/wizards/NewFromSMILESWizard.java : Use the molecule that is returned from the future. - http://git.io/QRc9Jw
07:34 egonw ok, excellent!
07:34 egonw ah, it's that easy?
07:35 egonw ok, but can you explain the code then?
07:35 egonw oh. wait... I think I got it...
07:35 egonw the code makes the thread block, but the Thread.sleep() ensures that it does not block other threads...
07:35 egonw that makes sense...
07:36 egonw so, just the GUI thread is blocked then?
07:36 egonw actually, since Kevin's code is so much faster than the old DeduceBondSystemTool, this can may even be removed...
07:36 egonw but let's not do that now...
07:52 Gpox actualy most of the method is wrapped in a job. The FutureTask is executed on a separate thread and the while -> sleep is there to advanced the progress monitor, we know how long it will take max becuase of the timeout
07:58 Gpox just noticed the setInterrupted should probably add that in there too. Maybe it should be http://stackoverflow.com/questions/4501223​/when-i-need-to-use-atomicboolean-in-java for thread safty
07:58 zarah Gpox's link is also http://tinyurl.com/c4zmna5
08:13 zaetnick joined #bioclipse
08:17 amarillion joined #bioclipse
08:19 jonalv joined #bioclipse
08:32 CIA-99 bioclipse.cheminformatics: Egon Willighagen 2.5.x * r8f2097d / plugins/net.bioclipse.cdk.business/src/ne​t/bioclipse/cdk/business/CDKManager.java : Use Kevin's double bond location finder in the cdk.fromSMILES() method - http://git.io/yiekVQ
08:32 CIA-99 bioclipse.cheminformatics: Egon Willighagen 2.5.x * r61a7aea / plugins/net.bioclipse.cdk.ui/src/net/biocli​pse/cdk/ui/wizards/NewFromSMILESWizard.java : Use Kevin's double bond location finder in the New from SMILES wizard, and removed the atom typing already done by the SMILES parsing. - http://git.io/iik2AA
09:30 olass joined #bioclipse
09:34 CIA-99 bioclipse.ds.models: Ola Spjuth master * racc5ed8 / features/net.bioclipse.ds.m​odels.r_feature/feature.xml : add feature deps - http://git.io/HqtbIw
09:44 CIA-99 bioclipse.ds.models: Ola Spjuth master * rbbb3d93 / features/net.bioclipse.ds.m​odels.r_feature/feature.xml : Added feature info - http://git.io/D8rN4g
09:45 CIA-99 bioclipse.ds: Ola Spjuth 2.5.x * r303fcfa / features/net.bioclipse.ds_feature/feature.xml : Update copyright year (+5 more commits...) - http://git.io/sDNU7Q
11:29 olass_ joined #bioclipse
11:53 Gpox joined #bioclipse
12:11 CIA-99 bioclipse.core: Valentin Georgiev 2.5.x * r8af489c / plugins/net.bioclipse.browser/src/net/biocli​pse/browser/views/ScrapingLabelProvider.java : solution addressing Bug 3223 from Arvid - http://git.io/j3rmHw
12:11 zarah bug #3223 | http://pele.farmbio.uu.se/bug​zilla36/show_bug.cgi?id=3223
12:11 CIA-99 bioclipse.core: goglepox 2.5.x * r1909992 / plugins/net.bioclipse.browser/src/net/biocli​pse/browser/views/ScrapingLabelProvider.java : Merge pull request #13 from valyo/2.5.x - http://git.io/x-2_DA
12:12 CIA-99 bioclipse.cheminformatics: Valentin Georgiev 2.5.x * r59635cc / (3 files in 3 dirs): Quick solution addressing Bug 3223 - http://git.io/zUnxBw
12:12 zarah bug #3223 | http://pele.farmbio.uu.se/bug​zilla36/show_bug.cgi?id=3223
12:12 CIA-99 bioclipse.cheminformatics: Valentin Georgiev 2.5.x * r67a1938 / (3 files in 2 dirs): Also quick but better solution addressing Bug 3223 from Arvid - http://git.io/9jPKSA
12:12 CIA-99 bioclipse.cheminformatics: goglepox 2.5.x * r845ca20 / (5 files in 4 dirs): Merge pull request #7 from valyo/2.5.x - http://git.io/bDvtpw
12:12 zarah bug #3223 | http://pele.farmbio.uu.se/bug​zilla36/show_bug.cgi?id=3223
12:47 andra joined #bioclipse
13:11 CIA-99 bioclipse.ds.models: Arvid Berg master * r41914c0 / features/net.bioclipse.ds.models.r_feature/p2.inf : The models.r feature can not be a category if is should be installed - http://git.io/o_Us-g
13:18 CIA-99 bioclipse.core: Arvid Berg 2.5.x * re104407 / plugins/net.bioclipse.ui.install/s​rc/net/bioclipse/ui/install/discov​ery/DSModelsDiscoveryStrategy.java : Changed query for DS discovery to include ds.models.r feature - http://git.io/FV_QmA
13:53 CIA-99 bioclipse.cheminformatics: Valentin Georgiev 2.5.x * r12aface / plugins/net.bioclipse.cdk.​business/build.properties : Bug 3223 again - add icons to build configurations - http://git.io/kvzXnA
13:53 CIA-99 bioclipse.cheminformatics: Jonathan Alvarsson 2.5.x * r9bed89a / plugins/net.bioclipse.cdk.​business/build.properties : Merge pull request #8 from valyo/2.5.x - http://git.io/AbzmPg
13:53 zarah bug #3223 | http://pele.farmbio.uu.se/bug​zilla36/show_bug.cgi?id=3223
14:08 iskywalker joined #bioclipse
14:09 iskywalker Hi!
14:09 zarah hello iskywalker, you fantastic person you
14:09 egonw hi iskywalker
14:10 iskywalker I am quite new to bioinformatics, I was wondering if there is a z-scale  (Sandberg) descriptor in bioclipse, or any available implementation of it
14:10 iskywalker I need it to calculate some features of proteins
14:14 egonw jonalv: what did the book say about that again?
14:15 jonalv egonw: it sounds familiar. But I am not sure what exists for the moment
14:20 iskywalker I think most of people are not sure what makes senses, but everything which somebdy tested should be somewhere so that others can learn from it...
14:20 iskywalker But seems, that there is no such database...
14:54 egonw iskywalker: can you please send an email to the mailing list?
14:54 egonw then I can forward it to the right person
16:10 zaetnick joined #bioclipse
19:01 egonw joined #bioclipse
19:05 sneumann_ joined #bioclipse

| Channels | #bioclipse index | Today | | Search | Google Search | Plain-Text | summary